large-scale integration of data and text
TRANSCRIPT
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Lars Juhl Jensen
Large-scale integration of data and text
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Lars Juhl Jensen
Large-scale integration of data and text
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Ph.D.
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sequence analysis
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postdoc
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staff scientist
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protein networks
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cellular signalling
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group leader
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cofounder
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data integration
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omics data
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association networks
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text mining
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biomedical literature
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electronic health records
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association networks
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guilt by association
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STRING
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Franceschini et al., Nucleic Acids Research, 2013
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1100+ genomes
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genomic context
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gene fusion
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Korbel et al., Nature Biotechnology, 2004
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operons
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Korbel et al., Nature Biotechnology, 2004
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bidirectional promoters
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Korbel et al., Nature Biotechnology, 2004
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phylogenetic profiles
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Korbel et al., Nature Biotechnology, 2004
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a real example
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Cell
Cellulosomes
Cellulose
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experimental data
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gene coexpression
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physical interactions
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Jensen & Bork, Science, 2008
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genetic interactions
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Beyer et al., Nature Reviews Genetics, 2007
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curated knowledge
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pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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many databases
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different formats
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different identifiers
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variable quality
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not comparable
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not same species
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hard work
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(Ph.D. students)
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quality scores
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von Mering et al., Nucleic Acids Research, 2005
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calibrate vs. gold standard
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von Mering et al., Nucleic Acids Research, 2005
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homology-based transfer
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Franceschini et al., Nucleic Acids Research, 2013
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missing most of the data
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text mining
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>10 km
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too much to read
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computer
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as smart as a dog
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teach it specific tricks
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named entity recognition
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comprehensive lexicon
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cyclin dependent kinase 1
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CDC2
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flexible matching
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cyclin dependent kinase 1
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cyclin-dependent kinase 1
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orthographic variation
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CDC2
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hCdc2
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“black list”
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SDS
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augmented browsing
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Reflect
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browser add-on
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real-time text mining
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009O’Donoghue et al., Journal of Web Semantics, 2010
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information extraction
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co-mentioning
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within documents
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within paragraphs
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within sentences
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NLPNatural Language Processing
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grammatical analysis
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Gene and protein namesCue words for entity recognitionVerbs for relation extraction
[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]
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more precise
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worse recall
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related web resources
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STITCH
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STRING + 300k chemicals
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stitch-db.org
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COMPARTMENTS
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compartments.jensenlab.org
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TISSUES
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tissues.jensenlab.org
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DISEASES
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diseases.jensenlab.org
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general framework
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curated knowledge
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experimental data
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text mining
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computational predictions
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common identifiers
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quality scores
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visualization
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web resources
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download files
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why so many?
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Swiss army knife syndrome
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targeted resources
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common infrastructure
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medical data mining
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Jensen et al., Nature Reviews Genetics, 2012
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opt-out
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opt-in
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centralized registries
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structured data
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Jensen et al., Nature Reviews Genetics, 2012
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14 years
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6.2 million patients
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119 million diagnoses
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distributions
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Jensen et al., submitted, 2014
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diagnosis trajectories
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Jensen et al., submitted, 2014
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Jensen et al., submitted, 2014
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complex trajectories
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Jensen et al., submitted, 2014
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confounding factors
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correlation ≠ causation
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electronic health records
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unstructured data
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Danish
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busy doctors
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pharmacovigilance
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custom dictionaries
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drugs
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adverse drug events
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typo rules
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complex filters
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Eriksson et al., Drug Safetey, 2014
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new adverse drug reactions
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Eriksson et al., Drug Safety, 2014
Drug substance ADE p-value
Chlordiazepoxide Nystagmus 4.0e-8
Simvastatin Personality changes
8.4e-8
Dipyridamole Visual impairment
4.4e-4
Citalopram Psychosis 8.8e-4
Bendroflumethiazide
Apoplexy 8.5e-3
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direct medical implications
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AcknowledgmentsSTRING/STITCHChristian von MeringDamian SzklarczykMichael KuhnManuel StarkSamuel ChaffronChris CreeveyJean MullerTobias DoerksPhilippe JulienAlexander RothMilan SimonovicJan KorbelBerend SnelMartijn HuynenPeer Bork
Text miningSune FrankildJasmin SaricEvangelos PafilisKalliopi TsafouAlberto SantosJanos BinderHeiko HornMichael KuhnNigel BrownReinhardt SchneiderSean O’ Donoghue
EHR miningAnders Boeck JensenPeter Bjødstrup JensenRobert ErikssonFrancisco S. RoqueHenriette SchmockMarlene DalgaardMassimo AndreattaThomas HansenKaren SøebySøren BredkjærAnders JuulTudor OpreaPope MoseleyThomas WergeSøren Brunak
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